Gut microbiota is known to play a main role in regulating both health and disease in humans. Strategies for the therapeutic modulation of gut microbiota are therefore expected to give a relevant contribution in the management of disorders associated with its impairment. Among these options, one of the most renowned is fecal microbiota transplantation (FMT). A growing body of evidence showed clearly that FMT is an effective treatment against recurrent Clostridium difficile infection. Moreover, it was shown to be a promising therapy for the management of several noncommunicable disorders, including inflammatory bowel diseases and metabolic disorders. Standardization of procedural protocols for different disorders will surely increase the therapeutic power of FMT. The aim of this narrative review was to make an overview of methodology, indications, and future perspectives of FMT for the management of disorders associated with gut microbiota impairment.